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2349  structures 5363  species 181  interactions 124478  sequences 3533  architectures

Clan: Ubiquitin (CL0072)

Summary

Ubiquitin superfamily Add an annotation

This family includes proteins that share the ubiquitin fold. It currently unites four SCOP superfamilies.

This clan contains 59 families and the total number of domains in the clan is 124478. The clan was built by A Bateman.

Members

This clan contains the following 59 member families:

APG12 APG5 Atg8 AUX_IAA Blt1 Caps_synth_GfcC CHIPS CIDE-N Cobl CRIM DCX DIX DUF2407 DUF3534 DUF4430 DWNN FERM_f0 FERM_N Flg_new GABP-alpha IgG_binding_B Lambda_tail_I Multi_ubiq NLE NQRA_SLBB Oxidored_molyb PB1 Phenol_monoox PI3K_p85B PI3K_rbd Prok_Ub RA Rad60-SLD Rad60-SLD_2 Ras_bdg_2 RAWUL RBD SAP18 SLBB Staphylokinase Telomere_Sde2 TGS ThiS ThiS-like TmoB TUG-UBL1 Ub-Mut7C Ub-RnfH ubiquitin Ubiquitin_2 Ubiquitin_3 UBX Ufm1 UN_NPL4 Urm1 USP7_C2 USP7_ICP0_bdg YchF-GTPase_C YukD

External database links

Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

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Alignments

The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
ubiquitin (PF00240) 21402 (17.2%) View
SLBB (PF10531) 11968 (9.6%) View
TGS (PF02824) 10791 (8.7%) View
ThiS (PF02597) 7014 (5.6%) View
RA (PF00788) 6093 (4.9%) View
Oxidored_molyb (PF00174) 5941 (4.8%) View
PB1 (PF00564) 5855 (4.7%) View
YchF-GTPase_C (PF06071) 5372 (4.3%) View
UBX (PF00789) 5113 (4.1%) View
FERM_N (PF09379) 4841 (3.9%) View
Flg_new (PF09479) 4615 (3.7%) View
AUX_IAA (PF02309) 3370 (2.7%) View
Rad60-SLD (PF11976) 2305 (1.9%) View
DCX (PF03607) 2143 (1.7%) View
Atg8 (PF02991) 2039 (1.6%) View
NLE (PF08154) 1420 (1.1%) View
USP7_C2 (PF14533) 1244 (1.0%) View
USP7_ICP0_bdg (PF12436) 1241 (1.0%) View
Ubiquitin_2 (PF14560) 1237 (1.0%) View
RBD (PF02196) 1128 (0.9%) View
DIX (PF00778) 1081 (0.9%) View
DUF4430 (PF14478) 1075 (0.9%) View
PI3K_rbd (PF00794) 1046 (0.8%) View
Rad60-SLD_2 (PF13881) 951 (0.8%) View
DWNN (PF08783) 926 (0.7%) View
RAWUL (PF16207) 908 (0.7%) View
Ub-RnfH (PF03658) 829 (0.7%) View
APG5 (PF04106) 817 (0.7%) View
SAP18 (PF06487) 742 (0.6%) View
Telomere_Sde2 (PF13019) 742 (0.6%) View
continued
Pfam family Num. domains Alignment
Urm1 (PF09138) 728 (0.6%) View
YukD (PF08817) 725 (0.6%) View
FERM_f0 (PF16511) 706 (0.6%) View
APG12 (PF04110) 694 (0.6%) View
NQRA_SLBB (PF11973) 688 (0.6%) View
CRIM (PF16978) 642 (0.5%) View
TUG-UBL1 (PF11470) 555 (0.4%) View
CIDE-N (PF02017) 552 (0.4%) View
PI3K_p85B (PF02192) 477 (0.4%) View
DUF3534 (PF12053) 469 (0.4%) View
UN_NPL4 (PF11543) 442 (0.4%) View
Ubiquitin_3 (PF14836) 418 (0.3%) View
Ub-Mut7C (PF14451) 379 (0.3%) View
Ras_bdg_2 (PF14847) 369 (0.3%) View
Caps_synth_GfcC (PF06251) 360 (0.3%) View
Ufm1 (PF03671) 347 (0.3%) View
DUF2407 (PF10302) 342 (0.3%) View
Cobl (PF09469) 275 (0.2%) View
Multi_ubiq (PF14452) 245 (0.2%) View
Blt1 (PF12754) 220 (0.2%) View
GABP-alpha (PF11620) 162 (0.1%) View
Lambda_tail_I (PF06805) 102 (0.1%) View
Prok_Ub (PF14454) 99 (0.1%) View
Phenol_monoox (PF04663) 95 (0.1%) View
ThiS-like (PF14453) 81 (0.1%) View
TmoB (PF06234) 39 (0.0%) View
Staphylokinase (PF02821) 10 (0.0%) View
IgG_binding_B (PF01378) 7 (0.0%) View
CHIPS (PF11434) 1 (0.0%) View
Total: 59 Total: 124478
No alignment ℹ
 

Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.

Family relationships

This diagram shows the relationships between members of this clan. More...

Species distribution

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This tree shows the occurrence of the domains in this clan across different species. More...

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Interactions

There are 181 interactions for this clan. More...

Interacting families
A B
APG12 APG12
APG5
APG5 APG12
APG5
Atg8 ATG19_autophagy
Atg8
Calreticulin
Blt1 Blt1
C1-set IgG_binding_B
CALCOCO1 Atg8
Caps_synth_GfcC Caps_synth_GfcC
CDC48_2 UBX
CDC48_N UBX
CIDE-N CIDE-N
Cobalamin_bind DUF4430
Complex1_51K SLBB
CUE ubiquitin
Cyt-b5 Oxidored_molyb
DIX DIX
DUF1952 ThiS
DUF4430 DUF4430
DUSP Ubiquitin_3
E1_UFD ubiquitin
E3_UbLigase_EDD ubiquitin
EF-hand_5 ubiquitin
FERM_C FERM_N
FERM_M FERM_N
FERM_N ERM
FERM_C
FERM_M
FERM_N
IRS
Flg_new Flg_new
Flu_B_NS1 ubiquitin
GAT ubiquitin
GFP ubiquitin
HECT ubiquitin
IgG_binding_B CRISPR_Cas2
IgG_binding_B
JAB ubiquitin
Josephin ubiquitin
KOW ubiquitin
MMR_HSR1 TGS
YchF-GTPase_C
MMR_HSR1_C TGS
Mo-co_dimer Oxidored_molyb
MoaE ThiS
OTU ubiquitin
Oxidored_molyb Cytochrom_C1
Cytochrome_CBB3
Mo-co_dimer
Oxidored_molyb
PALP ThiS
PB1 PB1
PCNA_C ubiquitin
Peptidase_C12 ubiquitin
Peptidase_C33 ubiquitin
Peptidase_C48 Rad60-SLD
ubiquitin
Peptidase_C54 Atg8
Peptidase_C65 ubiquitin
PI3_PI4_kinase PI3K_rbd
PI3K_rbd PI3_PI4_kinase
PI3K_rbd
PI3Ka
Ras
Pkinase PB1
Poly_export SLBB
Proteasom_Rpn13 ubiquitin
PX PB1
RA PH
RA
Ras
RasGEF
Rad60-SLD FKBP_C
IR1-M
Rad60-SLD
RanGAP1_C
ThiF
UQ_con
Ras RA
Ras_bdg_2
RBD
RBD RBD
Ribonuclease ubiquitin
Ribosomal_L14e ubiquitin
Ribosomal_L18A ubiquitin
Ribosomal_L29 ubiquitin
Ribosomal_L38e ubiquitin
RRM_1 SAP18
RS4NT ubiquitin
SAP18 SAP18
SH3_1 PB1
ubiquitin
SH3_9 ubiquitin
Skp1_POZ ubiquitin
SLBB 2Fe-2S_thioredx
NADH_4Fe-4S
Poly_export
SLBB
Staphylokinase Staphylokinase
TGS TGS
tRNA_SAD
ThiF Atg8
Rad60-SLD
ThiS
ubiquitin
ThiG ThiS
ThiS DUF1952
MoaE
ThiG
ThiS
Trypsin Staphylokinase
Tubulin DCX
Tubulin_C DCX
Ub-RnfH Ub-RnfH
UBA ubiquitin
UBA_e1_thiolCys Rad60-SLD
ubiquitin
ubiquitin BAG
CUE
Cullin_Nedd8
E3_UbLigase_EDD
Flu_B_NS1
GAT
IBR
JAB
KOW
NIF
OTU
PCNA_C
Peptidase_C12
Peptidase_C65
PFU
Ribosomal_L14e
Ribosomal_L18A
Ribosomal_L18p
Ribosomal_L30_N
Ribosomal_L40e
Ribosomal_L6
Ribosomal_S24e
Ribosomal_S27
Ribosomal_S28e
Ribosomal_S30
Ribosomal_S7
Ribosomal_S9
SART-1
SH3_9
Skp1_POZ
UBA
ubiquitin
UCH
UIM
UQ_con
VHS
Vps36_ESCRT-II
zf-A20
zf-RanBP
Ubiquitin_3 DUSP
UBX UBX
UCH ubiquitin
UDG Rad60-SLD
UEV ubiquitin
UIM ubiquitin
UN_NPL4 CDC48_2
CDC48_N
UQ_con Rad60-SLD
ubiquitin
USP7_ICP0_bdg USP7_C2
V-set ubiquitin
VHS ubiquitin
Vps36_ESCRT-II ubiquitin
YchF-GTPase_C MMR_HSR1
YchF-GTPase_C
YHS Phenol_monoox
TmoB
YukD YukD
zf-A20 ubiquitin
zf-C3HC4_3 ubiquitin
zf-RING_2 ubiquitin
zf-UBP ubiquitin

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

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